affxparser
Bioc currentAffymetrix File Parsing SDK
Release Lineage
Entered 1.7 · Oct 14, 2005
Current · Requires R 4.6
Description
Package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR). It provides methods for fast and memory efficient parsing of Affymetrix files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files are supported. Currently, there are methods for reading chip definition file (CDF) and a cell intensity file (CEL). These files can be read either in full or in part. For example, probe signals from a few probesets can be extracted very quickly from a set of CEL files into a convenient list structure.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
4258 0 exported
Complexity
8.8 avg / 76 max
Call network
4258 nodes / 3562 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
145,416
Files
716
Compiled share
89.1%
Has compiled src
Yes
Language breakdown
API
Exported functions
65
Internal functions
30
Testing
Has tests
Yes
Test-to-code ratio
0.10
testthat edition
–
Docs
Roxygen coverage
–
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
83.3%
Unsafe pattern score
0
Dep constraint coverage
–
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
2.14.0
System requirements
–
C++ standard
–
License
LGPL (>= 2)
License flags
SPDX valid, OSI approved
History
Versions
42
First release
2005-10-12
Latest release
2026-04-28
Avg cadence
183 days
Cold removal rate
100%
Dep drift
1
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 65 (31 internal)includes a package overview page
- Examples that run
- 95%19 run in a plain check · 1 never run
- Exported functions with examples
- 48%
- Documented parameters
- not tracked
- Return-value docs
- not tracked
- Help pages citing references
- 22%
Repository practices
5 development-tooling and community-health practices detected across 4 families in the upstream repository
Checks run against github.com/henrikbengtsson/affxparser on 2026-10-11.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
Topics
Depended on by (11)
Show all 14 packagesHide all 14 packages
Bioconductor (11)
Suggested by (3)
People
- Kasper Daniel Hansen author maintainer
- Henrik Bengtsson author
- James Bullard author
- Robert Gentleman contributor
- Jim Hester contributor
- Martin Morgan contributor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("affxparser")This package has no citation file, so citation() returns this entry built from DESCRIPTION.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.